Some days, you just want to give up the arguing and go rest your head on the desk for a while. No matter how dumb you think the opposition is, they’ll always manage to say something dumber than you can imagine.

This is “correlation is not causation” turned upside down and badly shaken. It’s one thing to say that just because there is a correlation you can’t say one thing is causal and another is caused. It’s quite another thing to say that is never the case. And it is quite another thing to say that DNA has nothing to do with amino acids, even a non-biologist like myself recognises that as bullshit.

[quote]
The amino acid sequence may be predicted or scientifically determined by a DNA sequence but this is an example of teleological determinism, not an example of the simple causal or functional determinism recognized by biology. DNA codes may contain stored information that is used in assembly of proteins and that stored information may predict or determine the amino acid sequence in the protein, but that is not the same as saying the DNA code causes the protein.

When biologists talk about DNA ‘determining’ or causing proteins and the complex structures and functions built from proteins, they are engaging in two types of intentional misrepresentation. First, they are suggesting or implying causal relationships far beyond anything supported by the evidence. The fact that a set of DNA is one component in one feature of protein assembly is very, very, different than suggesting that DNA is causing complex phenotypes and complex behaviors. Second, in claiming that DNA sequences determine protein sequences, they are implicitly using teleolgical intelligence based theories without admitting or recognizing what is being done.
[endquote]

Someone clarify this for me… is he saying that God performs miracles on my amino acids?

I think he might be referring to something like protein folding, which is poorly understood and apparently not “directly” coded for by the DNA sequence (as in prions). But that might be giving him far too much credit.

I’ve always casually thought of protein folding as analogous to public and private keys in encryption. Both keys suffice to determine the dog-awful big prime number used for encryption. But working backwards from that prime is only theoretically possible. So we know that DNA suffices for the protein, but given a specific protein we can’t yet work backwards to the DNA since we don’t know how folding works (very well). Is that analogy sound? Should I patent it?

The analogy is sort of correct… From the DNA sequence, we can determine the amino acid sequence of the protein. This amino acid sequence is what creates the complex structure. From that primary sequence, there are ways we can determine the major structural features without too much trouble, but figuring out exactly how it folds is a prohibitively difficult computational problem.

If, on the other hand, we know the amino acid sequence (a relatively easy thing to find), it’s possible to back-translate and search known sequences for something that would give your specific protein.

However, it’s impossible to determine the sequence of a protein or its gene from the structure. This never actually happens, since determining the structure of a given protein is difficult and usually won’t be done before the details of its sequence and gene are uncovered.

His implication that “DNA is [not] causing complex phenotypes and complex behaviors” is complete bullshit though. During the course of research, scientists selectively alter or disable genes to determine exactly what complicated phenotypic or behavioural effects are influenced by a gene.

DNA also codes for enzymes that ensure certain proteins fold into certain configurations. It would indeed be very difficult to produce such a system from scratch, especially if the folding chemicals were themselves the result of folding chemicals.

Such a system might eventually be bootstrapped into existence if simple biological systems could somehow become more complex in response to pressure from the environment — a basic system could produce more variations, with the most ‘successful’ variations perpetuating themselves and undergoing change over long periods of time. But there’s no process that can increase the complexity of such a biological system, so clearly it’s impossible.

These people already know everything they were told they needed to know. God is all they need to know. Every truth in existence has been written down inside that book written hundreds of years about by a bunch of virginal monks at the request of the king, based on copies of scrolls written over a thousand years earlier by a bunch of desert roaming nomads.

I remember having to attend church with my girlfriend whose parents were extreme fundies. She was good looking and rebellious. She put out so I went along with it. But to keep up appearances she insisted I go to church with her and her parents cause it kept them from bugging her about my ‘status in christ’.
The minister actually commented on our growing dependence on technology and went along with this sermon about how when you die and reserve your reward in heaven you can desire the greatest video game experience ever and it will come true. For all the D&D’ers who were in the audience he said that they’d be able to live an entire life in such an existence if it pleased them. Little girls would become Cinderella’s living in Disney like fairlylands. Anything you want. So we don’t need to become too dependent on video games and friends cause they will be in abundance in the afterlife. He also said we needn’t worry about knowing everything. If you study the bible closely enough every scientific answer will be provided. He even went off on some rant about how you can find the secret of PI found in the bible to 12 decimal places. Where he got that and where he got 12 decimal places worth of accuracy was amazing. I asked him about it afterwards and in a gruff reply stated that he wasn’t into science so he never looked himself. He just knew it was there cause some christian experts told him it was there.

I never did find out where and how, and I gave it up to a lie a long time ago.

But there you are. If you look hard enough in the passages there are codes and all kinds of shit that can tell you how to solve biology problems and quantum physics.
At least that’s what they want you to believe.

Um, Warren isn’t an engineer, his nom de ARN of “LifeEngineer” notwithstanding. He’s a retired actuary who once complained that he couldn’t read the professional literature because he didn’t have access to PubMed, obviously being unaware that it’s publicly available on the Web.

However, it’s impossible to determine the sequence of a protein or its gene from the structure.

Actually, it’s often fairly trivial to determine the sequence of a protein from its high-resolution X-ray crystallography structure. This is how structural biologists are often able to identify unexpected bound waters and other molecules in the structure. While it is not unheard of for a structural biologist to discover a mutation from the X-ray crystal before (s)he confirms it in the DNA sequence, I’ve never heard of a X-ray crystallography being used for complete sequencing–it’s way too hard.

Of course, you can’t get the DNA sequence from the protein structure due to the degeneracy of the DNA code, not the protein folding problem–the best you can do is try to match computational translations of known DNA sequences with your protein. The protein folding problem tells you why you cannot get an accurate structure just from the DNA (or protein) sequence–yet.

Actually, it’s often fairly trivial to determine the sequence of a protein from its high-resolution X-ray crystallography structure. This is how structural biologists are often able to identify unexpected bound waters and other molecules in the structure. While it is not unheard of for a structural biologist to discover a mutation from the X-ray crystal before (s)he confirms it in the DNA sequence, I’ve never heard of a X-ray crystallography being used for complete sequencing–it’s way too hard.

I have, using Xray crystallographic data, found errors in protein sequences.

I know people who have tried to determine the complete peptide sequence from just the crystallographic data. I was told the accuracy was around 60%. Some sidechains look a lot alike in density. Some sidechains, particularly on the surface of the protein, are not ordered. In some portions of the structure, especially the termini and surface loops, even the backbone may not be ordered.

It wouldn’t surprise me at all to find that most creationists, deep down, want to believe in some form of vitalism. It was lot more understandable to assume some kind of theism when life could only be viewed as a miracle beggaring all comprehension. The fact that life is actually composed of ordinary matter and energy, following ordinary naturalistic laws was a major blow to the entire idea of deriving religious belief from nature (as much as IDers love to talk about “machines”, such a view of life would probably have sounded like sacrilege less than 200 years ago). The current focus around evolution is purely a rear-guard action to save some little scrap of the miraculous.

What I find interesting is that if you took the IDers’ standard of proof as applied against evolution, you’d have to conclude that vitalism hasn’t been discredited either. After all, there are plenty of “gaps” in our understanding of exactly how some DNA sequence turns into a phenotype. That they do not emphasize these gaps shows not that they reject vitalism for any sound reason, but only that they’re too cowardly to take a stance that would be met with universal ridicule.

Implied in what I wrote above is that I would actually give this Warren Bergerson some credit for being less of a coward than many ID/creationists in admitting that he wants to believe in vitalism too. That doesn’t make his statement any less stupid, but it is probably more internally consistent than the notion that naturalism can explain the amazing process of development from cell to phenotype but will somehow inexplicably fail to explain the emergence of new species.

Molly: I agree, but I think it goes way beyond life science. I didn’t start paying attention to the whole ID nonsense till an article on Dembski and Behe appeared in the NYT about a year ago.

After trying to understand what Dembski was doing, it struck me that anyone who thinks evolution is inadequate to produce “designs” (or CSI or IC or whatever) would have to extend that inadequacy to all natural processes. Since they further suppose that humans are capable of design, the logical conclusion is that human intelligence is not a natural process. While that strikes me as a clear contradiction, I think that for Dembski that’s really the whole point. I have no doubt that Dembski is also an enemy of artificial intelligence research and indeed any attempt to understand cognition in terms of simpler, seemingly “unintelligent” processes.

The only reason that the IDers aren’t engaging in open warfare with the AI and cognitive science communities is that these subjects aren’t taught in the K-12 schools and don’t have the same visibility in the public debate. I am quite certain that if you could get an honest acknowledgement out of these guys, they’d concede that the latter subjects are at least as big a threat to their worldview as evolution.

PaulC: Johnson says his conflict is with materialism, doesn’t he? I’m actually surprised that the IDers haven’t stressed this more, since it would get a lot more religious sorts on their side, at least for a while.

Not to mention a large contingent of alties that that emphasis would bring in as well. I think the reason they haven’t tried that tactic is that they’re more concerned with keeping out the non-Christians than they are with expanding their base of support.

Hmm. I read something a number of years ago on “folding” in general. It seems that one of the complications in producing proteins in a lab, according to the article, is that while biological systems always fold the protein into a known configuration, mixing it in a jar gives you folding of “both” types, but you don’t get any that are “unfolded”. This has unintended consequences, in that the wrong folding can have no, opposite or completely different effects than the original substance. By Bergerson’s estimation, it should be “easier” to engineer the correct protein, than to allow organic processes to produce it. In reality, its the exact opposite, since those processes are required to “guarrentee” that it is folded correctly. The irony is, in some cases the people that stumbled on this, by noting that their lab made versions of some simple chemical didn’t have the effect the original plant based chemical had, found that the effect of the “incorrect” folding was greater or had some benefit the other form didn’t. Most labs, at the time of publication, discounted the difference (even scientists can occationally be stupid), waving off the idea that a mere difference in folding could have a notable, never mind drastic, effect on the patient. Some labs had begun to use processes to seperate the different foldings and test them seperately, while most continued to just scratch their heads, shrug their shoulders and proclaim, “Well, I guess the original tests with the purely orgnanic version must have been a fluke”.

Point being.. If DNA can’t be a direct cause of proteins, why would it be impossible for a lab to produce the “correct” form? Its totally ridiculous to claim such a thing.

Note: I don’t agree with the author’s ideas. So don’t jump on me. The following is merely an exercise in interpreting English text. See Andrey Fedorov’s question above.

The only sense I could derive from the following

[quote]
The amino acid sequence may be predicted or scientifically determined by a DNA sequence but this is an example of teleological determinism, not an example of the simple causal or functional determinism recognized by biology. DNA codes may contain stored information that is used in assembly of proteins and that stored information may predict or determine the amino acid sequence in the protein, but that is not the same as saying the DNA code causes the protein.
[/quote]

is that just as a bunch of bytes on a computer disk holding my photograph collection contain information that results in various pictures on the computer screen, the bunch of bytes is not the cause of the pictures; an entire apparatus intervenes between the bytes and the picture. The bytes encode the picture, but do not cause the picture. The author does not conceive that the code and its interpreter co-evolved; rather like the computer bytes, the decoding apparatus had to have been designed.

Regarding the following:

[quote]
When biologists talk about DNA ‘determining’ or causing proteins and the complex structures and functions built from proteins, they are engaging in two types of intentional misrepresentation. First, they are suggesting or implying causal relationships far beyond anything supported by the evidence. The fact that a set of DNA is one component in one feature of protein assembly is very, very, different than suggesting that DNA is causing complex phenotypes and complex behaviors.
[/quote]

the most charitable interpretation is that it is a warning against reductionism. When biologists talk about DNA determining or causing proteins, they really mean that DNA does this determination in the context of cellular apparatus, but perhaps there are people who don’t remember this and need to be warned.

Arun, yours is a most charitable interpretation. At worst this author is attempting to resurrect some flavor of vitalism.

And he’s not the only one who wants to supplant the causal determinism of DNA. Earlier in this thread I mentioned Vargas over on the ‘religious credulity’ thread – he’s been arguing against DNA also, apparently to supplant it with some flavor of environmental determinism – the ancient battle. But Vargas is gone for the w/e and that thread is pretty bloated and distorted anyway. I hope he shows up here.

More generally, the environmental determinists have the ear of post-modernists and other new-agers – anything to escape the apparent determinism of the selfish gene.

Arun is basically correct, though one could add that the author is basically equivocating on the meaning of “determine”. One sense is something like “cause” (see Bunge, Causality and Modern Science, for example). Another expresses a relationship like functional dependence. It is in this sense that the nucleotide sequence determines proteins.

DISCLAIMER: SCREW ID. I hate it.
Now that we have that out of the way….
I do think not enough attention is payed to the environment, but I do not pretend to incurr in “environmental determinism”. To say the environment “instructs” what goes on in the organsim is as silly to me as to say the DNA “instructs”
DNA may determine the primary sequence of a protein. This may allow and constrain aspects of folding, but it is not determining of a given result. As we know, other than the gene, the context is relevant, specially other protein folding enzymes whose action is actually not negligible, but extensive.
If you want, you can go a step back, because between the DNA sequence and the protein there is mRNA, and mRNA can be edited to produce different proteins depending again on other than the DNA: the context. And whether the mRNA will be available for translation depends on microRNA’s that may bind to it and degrade it.
But then lets take yet another step back to transcription. Again it does not depend on the gene, but on the context, the presence of enhancers, transcription factors…not to mention methilation…and then of course there is all the trasncrition machinery and enzimes we just take for granted.
So that we may go from primary DNA sequence to a given protein, actually requires for several “causes” beyond the sequence of DNA that infleucnes the primary sequence of DNA.

You may think that at each moment, the right stuff is at the apporpiate place because of an aspect of the primary sequence of DNA somewhere else in the genome… such that in the end there is just arrows in one direction, form the pupetter DNA, which provides the information, to the puppet, basically, “everything that goes on in the cell”…
OR you can realize that DNA is in a network of arrows in all directions, with many recursive loops, and that these interactiosn are what allow it or not to participate in the synthesis of a given protein.